[single molecule] obabel whatever.smi --gen3d -O whatever.sdf [batch] obabel smiles.smi --gen3d -O ligand*.pdb
[convert single molecule from SMILES to pdb] molconvert -3 pdb taxol.smi -o taxol.pdb
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Docking Experiments
Docking runs against various targets can be found hereOpen Source Software Used in Docking Work Flow
Pocket Detection
fpocket
linkSPPIDER
linkConformer Generation
Frog2
link - see also this listDocking Programs
AutoDoc Vina
linkPyRX (gui that uses vina, open babel, etc)
FRED
linkTHINK
Docking Descriptions and Experimentslink
Arguslab
linkQuantum
linkOOPSE (from Open Source Science Project)
linkMolecular Minimization
Open Babel
MOPAC
Open Source Version 7Marvin
SubStructure Searching
OpenBabel
tutorialMarvin